I agree with wid, on a strict $1000 budget Axioms all around will be difficult.

How about getting the Onk HTIB I mentioned above, add a nice pair of front speakers that will blend well with the Onk bookshelves (maybe some Wharfedale Diamond 2.4s?) and scrap the 3 cheapy surrounds that Onkyo gives you? The weak link will be the center channel (pretty boxy from my brief in store demo), but the rest of it will be pretty damn good.